For a selected list of genes from any GeneChip, derives the physical position on the model genomes(rice or Arabidopsis) with supporting information from predicted ORF and full-length cDNA; can view gene structures and retrieve corresponding sequences.

Data normalization was carried out by a script using Bioconductor and R.

Bioconductor/R :
Bioconductor is an open source project
for microarray data analysis, visualization and annotation.
It started in
fall of 2001 and quickly evolved into a high-profile
project. It provides packages for analyzing both
Affymetrix GeneChip data (affy, affydata and
affycomp packages) and cDNA spotted microarrays.
PLEXdb uses its affy package for estimation of
expression values by Robust Multi-chip Average (RMA)
and MAS5.0 methods. A
note
from Dr. Dan Nettleton demonstrates how RMA estimation is carried out.

R is a GNU project. It is an
open source language and environment for statistical computing.
R is a functional programming language and has powerful
graphical and visualization capabilities. Bioconductor is
developed with R.

MAS5.0: Affymetrix
provides with its Microarray Analysis Suite 5.0 the function to
do absolute and comparative expression estimation. MAS5.0 uses
statistical algorithm for normalization and calculate the
expression values, the presence/absence call and the p-values of
calls.

dChip:
This is one of the most common normalization
methods for estimating expression signals. It is free
for academic use, though it is not open source. dChip
used model-based estimate for gene expression indeces
(MBEI), which was proposed by Li and Wong (2001).
Bioconductor has a very rough approximation of
dChip's method. dChip is not used in PLEXdb.

The Power Atlas is a
web-based resource to assist investigators in the planning and
design of microarray and expression based experiments. This
software is currently aimed at estimating the power and sample size
for a two-group comparison based upon pilot data.

Genomics Data
Exploration Tools

Model Genome Interrogator
This tool allows the user to input a selected list of genes from a
microarray to derive the physical position on the rice and Arabidopsis
thaliana genomes with hyperlinks to the alignments on the
GRAMENE rice and the
TAIRArabidopsis thaliana browsers.

MapViewer
and SeqViewer
are two complementary visualization tools developed
by TAIR for
integrative exploration of the genetic and physical
maps, markers, sequences and other annotation
information concerning Arabidopsis.

SeqViewer permits searching for names or
short sequences and viewing hits against the whole
genome. MapViewer works from the other direction, letting
users select chromosomes or segments, locating relevant
makers, clones and gene sequence information.

General Purpose Data
Visualization Tools

GGobi:The GGobi software is
a system for the visualization of high-dimensional data.
It can be directly
accessed from R, Perl or Python. It
supports databases like Postgres and MySQL and can
support XML formatted data.

MATLAB:
MATLAB is a commercial high-level language that
integrates mathematical computing and visualization.
Similar to R, it is easily extensible by the user.

S-PLUS: This is the
commercial counterpart of R, an
implementation of the S programming language.

Manet :
MANET is Macintosh-based software for interactive
visualization for studying multivariate features of
data sets with missing values.